rs1555865385

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM4_SupportingPP5

The NM_152296.5(ATP1A3):​c.410_412delCCT​(p.Ser137del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 31)

Consequence

ATP1A3
NM_152296.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2U:1

Conservation

PhyloP100: 9.97
Variant links:
Genes affected
ATP1A3 (HGNC:801): (ATPase Na+/K+ transporting subunit alpha 3) The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of Na+/K+ -ATPases. Na+/K+ -ATPase is an integral membrane protein responsible for establishing and maintaining the electrochemical gradients of Na and K ions across the plasma membrane. These gradients are essential for osmoregulation, for sodium-coupled transport of a variety of organic and inorganic molecules, and for electrical excitability of nerve and muscle. This enzyme is composed of two subunits, a large catalytic subunit (alpha) and a smaller glycoprotein subunit (beta). The catalytic subunit of Na+/K+ -ATPase is encoded by multiple genes. This gene encodes an alpha 3 subunit. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM1
In a transmembrane_region Helical (size 20) in uniprot entity AT1A3_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_152296.5
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_152296.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 19-41986174-TAGG-T is Pathogenic according to our data. Variant chr19-41986174-TAGG-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 503717.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Likely_pathogenic=2}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ATP1A3NM_152296.5 linkuse as main transcriptc.410_412delCCT p.Ser137del disruptive_inframe_deletion 5/23 ENST00000648268.1 NP_689509.1 P13637-1Q53ES0
ATP1A3NM_001256214.2 linkuse as main transcriptc.449_451delCCT p.Ser150del disruptive_inframe_deletion 5/23 NP_001243143.1 P13637-3Q53ES0
ATP1A3NM_001256213.2 linkuse as main transcriptc.443_445delCCT p.Ser148del disruptive_inframe_deletion 5/23 NP_001243142.1 P13637-2Q53ES0
ATP1A3XM_047438862.1 linkuse as main transcriptc.320_322delCCT p.Ser107del disruptive_inframe_deletion 5/23 XP_047294818.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ATP1A3ENST00000648268.1 linkuse as main transcriptc.410_412delCCT p.Ser137del disruptive_inframe_deletion 5/23 NM_152296.5 ENSP00000498113.1 P13637-1
ENSG00000285505ENST00000644613.1 linkuse as main transcriptn.410_412delCCT non_coding_transcript_exon_variant 5/25 ENSP00000494711.1 A0A2R8YEY8

Frequencies

GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

ATP1A3-associated neurological disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingMolecular Genetics, Royal Melbourne HospitalNov 11, 2021This sequence change is predicted to cause a change in the length of the protein due to an in-frame deletion of one amino acid in a non-repeat region of the ATP1A3 protein (p.(Ser137del)). The region deleted is highly conserved (100 vertebrates, UCSC), and is located in a transmembrane helical region. This variant is absent from gnomAD v2.1 and v3.1. This variant has been reported in at least two probands with dystonia-parkinsonism, and has been reported to segregate with disease in eight affected family members from a single family (Royal Melbourne Hospital; PMID: 25359261, described as c.443_445delGAG, p.Ser148del). It has been classified as a variant of uncertain significance and likely pathogenic (ClinVar ID: 503717). Furthermore, two missense variants at the same position (p.Ser137Phe and p.Ser137Tyr) have been identified in cases with alternating hemiplegia of childhood (PMID: 22842232). Based on the classification scheme RMH Modified ACMG Guidelines v1.4.0, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PP1_Strong, PS4_Supporting, PM2_Supporting, PM4_Supporting. -
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingGeneDxJan 25, 2018The c.410_412delCCT variant in the ATP1A3 gene has been reported previously to segregate in a family with dystonia, with one unaffected family member also reported to harbor the c.410_412delCCT variant suggesting reduced penetrance for this variant (Wilcox et al., 2014). This variant causes an in-frame deletion of codon Serine 137, denoted p.Ser137del. The c.410_412delCCT variant is not observed in large population cohorts (Lek et al., 2016). In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. We interpret c.410_412delCCT as a likely pathogenic variant. -
Dystonia 12 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 09, 2017In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. This variant has been reported to segregate with disease in a single family affected with dystonia (PMID: 25359261). This variant is also referred to as c.443_445del (p.Ser148del) in the literature. This variant is not present in population databases (ExAC no frequency). This variant, c.410_412delCCT, results in the deletion of 1 amino acid(s) of the ATP1A3 protein (p.Ser137del), but otherwise preserves the integrity of the reading frame. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555865385; hg19: chr19-42490326; API